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Question: Set unified genotyper for bacterial genomes
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gravatar for aurelie.renvoise
4.4 years ago by
aurelie.renvoise • 10
aurelie.renvoise • 10 wrote:

Hello,

could someone tell me how to set the ploidy of unified genotyper to 1, to run it for bacterial genomes?

Thanks a lot,

Aurelie
snp • 1.1k views
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modified 4.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.4 years ago by aurelie.renvoise • 10
0
gravatar for Jennifer Hillman Jackson
4.4 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

You will need to do this on a cloud instance, using the "gatk2" repository from the Tool Shed (the GATK tool versions on the public Main Galaxy http://usegalaxy.org are 1.4). 

http://usegalaxy.org/cloud
http://toolshed.g2.bx.psu.edu/
http://usegalaxy.org/toolshed

Alternatives may include some other public Galaxy instances that have GATK2 installed and enough quota for you to do your work. You can search a list of known sites here:

http://wiki.galaxyproject.org/PublicGalaxyServers

Best, Jen, Galaxy team
ADD COMMENT • link modified 4.4 years ago • written 4.4 years ago by Jennifer Hillman Jackson ♦ 25k
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